Genetic Variant DRAIC:n.1229+817C>T (chr15-69793977-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000647319.1(DRAIC):n.1229+817C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.752 in 151,962 control chromosomes in the GnomAD database, including 43,820 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.75 ( 43820 hom., cov: 30)

Consequence

DRAIC
ENST00000647319.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.04

Publications

3 publications found

Variant links:

Genes affected

DRAIC (HGNC:27082): (downregulated RNA in cancer, inhibitor of cell invasion and migration)

DRAIC links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.79).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.823 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
DRAIC	ENST00000647319.1 link	n.1229+817C>T	intron_variant	Intron 10 of 11
DRAIC	ENST00000798860.1 link	n.127+37771C>T	intron_variant	Intron 2 of 3
DRAIC	ENST00000798861.1 link	n.106+37771C>T	intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.752

AC:

114261

AN:

151844

Hom.:

43806

Cov.:

show subpopulations

Gnomad AFR

AF:

0.687

Gnomad AMI

AF:

0.950

Gnomad AMR

AF:

0.688

Gnomad ASJ

AF:

0.759

Gnomad EAS

AF:

0.412

Gnomad SAS

AF:

0.603

Gnomad FIN

AF:

0.823

Gnomad MID

AF:

0.753

Gnomad NFE

AF:

0.829

Gnomad OTH

AF:

0.756

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.752

AC:

114311

AN:

151962

Hom.:

43820

Cov.:

AF XY:

0.746

AC XY:

55432

AN XY:

74274

show subpopulations

African (AFR)

AF:

0.687

AC:

28445

AN:

41392

American (AMR)

AF:

0.688

AC:

10501

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.759

AC:

2634

AN:

3472

East Asian (EAS)

AF:

0.412

AC:

2119

AN:

5148

South Asian (SAS)

AF:

0.604

AC:

2897

AN:

4800

European-Finnish (FIN)

AF:

0.823

AC:

8706

AN:

10576

Middle Eastern (MID)

AF:

0.745

AC:

219

AN:

294

European-Non Finnish (NFE)

AF:

0.829

AC:

56346

AN:

67990

Other (OTH)

AF:

0.749

AC:

1578

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1367

2735

4102

5470

6837

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

838

1676

2514

3352

4190

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.791

Hom.:

76663

Bravo

AF:

0.737

Asia WGS

AF:

0.529

AC:

1844

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

0.20

(source)

DANN

Benign

0.68

PhyloP100

-2.0

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over